Table 5.
Five known copy number differences detected between parental strains using WGS read depth.
| Chromosome | Type | No. of 2.5 kb windows | Significant windows (p < 0.001) | Highest Chi-square value |
|---|---|---|---|---|
| 2 | Deletion - in both | 15 | 0 | 3.99 |
| 5 | Amplification - 7C126 | 33 | 33 | 1212 |
| 9 | Deletion - in both | 52 | 13 | 50.6 |
| 12 | Amplification - 7C126 | 1 | 1 | 85.44 |
| 12 | Amplification - SC05 | 64 | 63 | 356.03 |
Read alignment density was consistent with the known CNV alleles except for chromosome 9, where smaller insertions and deletions are detected within a larger shared allele.